It seems that there is some evidence that the effects of autism can be altered by TMS. This is news to me, I am going to have to do a little Pub Med sleuthing to see what the word on the scientific street is.
It would make sense that by altering an already skewed balance of hyper and hypo excitability you would be able to alter the balance of the brain activity.
Turns out there is a total dearth of science regarding TMS as a treatment for autism. A PubMed search only gave me one article that was in a journal of scientific hypotheses.
Here is the article from about.com